spacr 0.1.81__py3-none-any.whl → 0.2.0__py3-none-any.whl

spacr/gui_elements.py

@@ -14,23 +14,105 @@ from collections import deque
 from skimage.draw import polygon, line
 from skimage.transform import resize
 from scipy.ndimage import binary_fill_holes, label
+from tkinter import ttk, scrolledtext
+import platform
+
+def set_dark_style(style, parent_frame=None, containers=None, widgets=None, font_family="Arial", font_size=12, bg_color='black', fg_color='white', active_color='blue', inactive_color='dark_gray'):
+    
+    if platform.system() == 'Darwin':
+        bg_color = '#313131'
+    else:
+        bg_color = '#000000'
+
+    if active_color == 'teal':
+        active_color = '#008080'
+    if inactive_color == 'dark_gray':
+        inactive_color = '#050505'
+    if bg_color == 'black':
+        bg_color = '#000000'
+    if fg_color == 'white':
+        fg_color = '#ffffff'
+    if active_color == 'blue':
+        active_color = '#007BFF'
+
+    font_style = tkFont.Font(family=font_family, size=font_size)
+    style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', fieldbackground=bg_color, foreground=fg_color, font=font_style)
+    style.configure('TCombobox', fieldbackground=bg_color, background=bg_color, foreground=fg_color, selectbackground=bg_color, selectforeground=fg_color, font=font_style)
+    style.map('TCombobox', fieldbackground=[('readonly', bg_color)], foreground=[('readonly', fg_color)], selectbackground=[('readonly', bg_color)], selectforeground=[('readonly', fg_color)])
+    style.configure('Custom.TButton', background=bg_color, foreground=fg_color, bordercolor=fg_color, focusthickness=3, focuscolor=fg_color, font=(font_family, font_size))
+    style.map('Custom.TButton', background=[('active', active_color), ('!active', bg_color)], foreground=[('active', fg_color), ('!active', fg_color)], bordercolor=[('active', fg_color), ('!active', fg_color)])
+    style.configure('Custom.TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background=bg_color, foreground=fg_color, font=font_style)
+    style.configure('Spacr.TCheckbutton', background=bg_color, foreground=fg_color, indicatoron=False, relief='flat', font="15")
+    style.map('Spacr.TCheckbutton', background=[('selected', bg_color), ('active', bg_color)], foreground=[('selected', fg_color), ('active', fg_color)])
+    style.configure('TLabel', background=bg_color, foreground=fg_color, font=font_style)
+    style.configure('TFrame', background=bg_color)
+    style.configure('TPanedwindow', background=bg_color)
+    style.configure('TNotebook', background=bg_color, tabmargins=[2, 5, 2, 0])
+    style.configure('TNotebook.Tab', background=bg_color, foreground=fg_color, padding=[5, 5], font=font_style)
+    style.map('TNotebook.Tab', background=[('selected', active_color), ('active', active_color)], foreground=[('selected', fg_color), ('active', fg_color)])
+    style.configure('TButton', background=bg_color, foreground=fg_color, padding='5 5 5 5', font=font_style)
+    style.map('TButton', background=[('active', active_color), ('disabled', inactive_color)])
+    style.configure('Vertical.TScrollbar', background=bg_color, troughcolor=bg_color, bordercolor=bg_color)
+    style.configure('Horizontal.TScrollbar', background=bg_color, troughcolor=bg_color, bordercolor=bg_color)
+    style.configure('Custom.TLabelFrame', font=(font_family, font_size, 'bold'), background=bg_color, foreground='white', relief='solid', borderwidth=1)
+    style.configure('Custom.TLabelFrame.Label', background=bg_color, foreground='white', font=(font_family, font_size, 'bold'))
+
+    if parent_frame:
+        parent_frame.configure(bg=bg_color)
+        parent_frame.grid_rowconfigure(0, weight=1)
+        parent_frame.grid_columnconfigure(0, weight=1)
+
+    if containers:
+        for container in containers:
+            if isinstance(container, ttk.Frame):
+                container_style = ttk.Style()
+                container_style.configure(f'{container.winfo_class()}.TFrame', background=bg_color)
+                container.configure(style=f'{container.winfo_class()}.TFrame')
+            else:
+                container.configure(bg=bg_color)
+
+    if widgets:
+        for widget in widgets:
+            if isinstance(widget, (tk.Label, tk.Button, tk.Frame, ttk.LabelFrame, tk.Canvas)):
+                widget.configure(bg=bg_color)
+            if isinstance(widget, (tk.Label, tk.Button)):
+                widget.configure(fg=fg_color, font=(font_family, font_size))
+            if isinstance(widget, scrolledtext.ScrolledText):
+                widget.configure(bg=bg_color, fg=fg_color, insertbackground=fg_color)
+            if isinstance(widget, tk.OptionMenu):
+                widget.configure(bg=bg_color, fg=fg_color, font=(font_family, font_size))
+                menu = widget['menu']
+                menu.configure(bg=bg_color, fg=fg_color, font=(font_family, font_size))
+
+    return {'font_family': font_family, 'font_size': font_size, 'bg_color': bg_color, 'fg_color': fg_color, 'active_color': active_color, 'inactive_color': inactive_color}
+
+def set_default_font(root, font_name="Arial", size=12):
+    default_font = (font_name, size)
+    root.option_add("*Font", default_font)
+    root.option_add("*TButton.Font", default_font)
+    root.option_add("*TLabel.Font", default_font)
+    root.option_add("*TEntry.Font", default_font)
 
 class spacrDropdownMenu(tk.OptionMenu):
     def __init__(self, parent, variable, options, command=None, **kwargs):
         self.variable = variable
         self.variable.set("Select Category")
         super().__init__(parent, self.variable, *options, command=command, **kwargs)
-        self.config(bg='black', fg='white', font=('Helvetica', 12), indicatoron=0)
+        self.update_styles()
+
+    def update_styles(self, active_categories=None):
+        style = ttk.Style()
+        style_out = set_dark_style(style, widgets=[self])
         self.menu = self['menu']
-        self.menu.config(bg='black', fg='white', font=('Helvetica', 12))
+        style_out = set_dark_style(style, widgets=[self.menu])
 
-    def update_styles(self, active_categories):
-        menu = self['menu']
-        for idx, option in enumerate(self['menu'].entrycget(idx, "label") for idx in range(self['menu'].index("end")+1)):
-            if option in active_categories:
-                menu.entryconfig(idx, background='teal', foreground='white')
-            else:
-                menu.entryconfig(idx, background='black', foreground='white')
+        if active_categories is not None:
+            for idx in range(self.menu.index("end") + 1):
+                option = self.menu.entrycget(idx, "label")
+                if option in active_categories:
+                    self.menu.entryconfig(idx, background=style_out['active_color'], foreground=style_out['fg_color'])
+                else:
+                    self.menu.entryconfig(idx, background=style_out['bg_color'], foreground=style_out['fg_color'])
 
 class spacrCheckbutton(ttk.Checkbutton):
     def __init__(self, parent, text="", variable=None, command=None, *args, **kwargs):
@@ -39,6 +121,8 @@ class spacrCheckbutton(ttk.Checkbutton):
         self.variable = variable if variable else tk.BooleanVar()
         self.command = command
         self.configure(text=self.text, variable=self.variable, command=self.command, style='Spacr.TCheckbutton')
+        style = ttk.Style()
+        _ = set_dark_style(style, widgets=[self])
 
 class spacrFrame(ttk.Frame):
     def __init__(self, container, width=None, *args, bg='black', **kwargs):
@@ -65,25 +149,25 @@ class spacrFrame(ttk.Frame):
         self.grid_columnconfigure(0, weight=1)
         self.grid_columnconfigure(1, weight=0)
         
-        for child in self.scrollable_frame.winfo_children():
-            child.configure(bg='black')
+        style = ttk.Style()
+        _ = set_dark_style(style, containers=[self], widgets=[canvas, scrollbar, self.scrollable_frame])
 
 class spacrLabel(tk.Frame):
     def __init__(self, parent, text="", font=None, style=None, align="right", **kwargs):
-        label_kwargs = {k: v for k, v in kwargs.items() if k in ['foreground', 'background', 'font', 'anchor', 'justify', 'wraplength']}
-        for key in label_kwargs.keys():
-            kwargs.pop(key)
-        super().__init__(parent, **kwargs)
+        valid_kwargs = {k: v for k, v in kwargs.items() if k not in ['foreground', 'background', 'font', 'anchor', 'justify', 'wraplength']}
+        super().__init__(parent, **valid_kwargs)
+        
         self.text = text
-        self.kwargs = label_kwargs
         self.align = align
         screen_height = self.winfo_screenheight()
         label_height = screen_height // 50
         label_width = label_height * 10
-        self.canvas = tk.Canvas(self, width=label_width, height=label_height, highlightthickness=0, bg=self.kwargs.get("background", "black"))
+        style_out = set_dark_style(ttk.Style())
+
+        self.canvas = tk.Canvas(self, width=label_width, height=label_height, highlightthickness=0, bg=style_out['bg_color'])
         self.canvas.grid(row=0, column=0, sticky="ew")
 
-        self.font_style = font if font else tkFont.Font(family=self.kwargs.get("font_family", "Helvetica"), size=self.kwargs.get("font_size", 12), weight=tkFont.NORMAL)
+        self.font_style = font if font else tkFont.Font(family=style_out['font_family'], size=style_out['font_size'], weight=tkFont.NORMAL)
         self.style = style
 
         if self.align == "center":
@@ -95,13 +179,15 @@ class spacrLabel(tk.Frame):
 
         if self.style:
             ttk_style = ttk.Style()
-            ttk_style.configure(self.style, **label_kwargs)
-            self.label_text = ttk.Label(self.canvas, text=self.text, style=self.style, anchor=text_anchor, justify=text_anchor)
+            ttk_style.configure(self.style, font=self.font_style, background=style_out['bg_color'], foreground=style_out['fg_color'])
+            self.label_text = ttk.Label(self.canvas, text=self.text, style=self.style, anchor=text_anchor)
             self.label_text.pack(fill=tk.BOTH, expand=True)
         else:
             self.label_text = self.canvas.create_text(label_width // 2 if self.align == "center" else label_width - 5, 
-                                                      label_height // 2, text=self.text, fill=self.kwargs.get("foreground", "white"), 
+                                                      label_height // 2, text=self.text, fill=style_out['fg_color'], 
                                                       font=self.font_style, anchor=anchor_value, justify=tk.RIGHT)
+        
+        _ = set_dark_style(ttk.Style(), containers=[self], widgets=[self.canvas])
 
     def set_text(self, text):
         if self.style:
@@ -110,24 +196,40 @@ class spacrLabel(tk.Frame):
             self.canvas.itemconfig(self.label_text, text=text)
 
 class spacrButton(tk.Frame):
-    def __init__(self, parent, text="", command=None, font=None, *args, **kwargs):
+    def __init__(self, parent, text="", command=None, font=None, icon_name=None, size=50, show_text=True, outline=True, *args, **kwargs):
         super().__init__(parent, *args, **kwargs)
-        self.text = text
+        
+        self.text = text.capitalize()  # Capitalize only the first letter of the text
         self.command = command
-        #screen_height = self.winfo_screenheight()
-        button_height = 50 #screen_height // 50
-        button_width = 140 #button_height * 3
+        self.icon_name = icon_name if icon_name else text.lower()
+        self.size = size
+        self.show_text = show_text
+        self.outline = outline
+
+        style_out = set_dark_style(ttk.Style())
 
-        #print(button_height, button_width)
+        if self.show_text:
+            self.button_width = int(size * 3)
+        else:
+            self.button_width = self.size  # Make the button width equal to the size if show_text is False
 
-        # Increase the canvas size to accommodate the button and the rim
-        self.canvas = tk.Canvas(self, width=button_width + 4, height=button_height + 4, highlightthickness=0, bg="black")
+        # Create the canvas first
+        self.canvas = tk.Canvas(self, width=self.button_width + 4, height=self.size + 4, highlightthickness=0, bg=style_out['bg_color'])
         self.canvas.grid(row=0, column=0)
 
-        self.button_bg = self.create_rounded_rectangle(2, 2, button_width + 2, button_height + 2, radius=20, fill="#000000", outline="#ffffff")
+        # Apply dark style and get color settings
+        color_settings = set_dark_style(ttk.Style(), containers=[self], widgets=[self.canvas])
 
-        self.font_style = font if font else tkFont.Font(family="Helvetica", size=12, weight=tkFont.NORMAL)
-        self.button_text = self.canvas.create_text((button_width + 4) // 2, (button_height + 4) // 2, text=self.text, fill="white", font=self.font_style)
+        if self.outline:
+            self.button_bg = self.create_rounded_rectangle(2, 2, self.button_width + 2, self.size + 2, radius=20, fill=color_settings['bg_color'], outline=color_settings['fg_color'])
+        else:
+            self.button_bg = self.create_rounded_rectangle(2, 2, self.button_width + 2, self.size + 2, radius=20, fill=color_settings['bg_color'], outline=color_settings['bg_color'])
+        
+        self.load_icon()
+        self.font_style = font if font else ("Arial", 12)  # Default font if not provided
+        
+        if self.show_text:
+            self.button_text = self.canvas.create_text(self.size + 10, self.size // 2 + 2, text=self.text, fill=color_settings['fg_color'], font=self.font_style, anchor="w")  # Align text to the left of the specified point
 
         self.bind("<Enter>", self.on_enter)
         self.bind("<Leave>", self.on_leave)
@@ -136,11 +238,45 @@ class spacrButton(tk.Frame):
         self.canvas.bind("<Leave>", self.on_leave)
         self.canvas.bind("<Button-1>", self.on_click)
 
+        self.bg_color = color_settings['bg_color']
+        self.active_color = color_settings['active_color']
+        self.fg_color = color_settings['fg_color']
+        self.is_zoomed_in = False  # Track zoom state for smooth transitions
+
+    def load_icon(self):
+        icon_path = self.get_icon_path(self.icon_name)
+        try:
+            icon_image = Image.open(icon_path)
+        except (FileNotFoundError, Image.UnidentifiedImageError):
+            try:
+                icon_path = icon_path.replace(' ', '_')
+                icon_image = Image.open(icon_path)
+            except (FileNotFoundError, Image.UnidentifiedImageError):
+                icon_image = Image.open(self.get_icon_path("default"))
+                print(f'Icon not found: {icon_path}. Using default icon instead.')
+
+        initial_size = int(self.size * 0.9)  # Make the initial size slightly smaller
+        self.original_icon_image = icon_image.resize((initial_size, initial_size), Image.Resampling.LANCZOS)
+        self.icon_photo = ImageTk.PhotoImage(self.original_icon_image)
+
+        self.button_icon = self.canvas.create_image(self.size // 2 + 2, self.size // 2 + 2, image=self.icon_photo)
+        self.canvas.image = self.icon_photo  # Keep a reference to avoid garbage collection
+
+    def get_icon_path(self, icon_name):
+        icon_dir = os.path.join(os.path.dirname(__file__), 'resources', 'icons')
+        return os.path.join(icon_dir, f"{icon_name}.png")
+
     def on_enter(self, event=None):
-        self.canvas.itemconfig(self.button_bg, fill="#008080")  # Teal color
+        self.canvas.itemconfig(self.button_bg, fill=self.active_color)
+        self.update_description(event)
+        if not self.is_zoomed_in:
+            self.animate_zoom(1.1)  # Zoom in the icon by 10%
 
     def on_leave(self, event=None):
-        self.canvas.itemconfig(self.button_bg, fill="#000000")  # Black color
+        self.canvas.itemconfig(self.button_bg, fill=self.bg_color)
+        self.clear_description(event)
+        if self.is_zoomed_in:
+            self.animate_zoom(1.0)  # Reset the icon size
 
     def on_click(self, event=None):
         if self.command:
@@ -148,18 +284,15 @@ class spacrButton(tk.Frame):
 
     def create_rounded_rectangle(self, x1, y1, x2, y2, radius=20, **kwargs):
         points = [
-            x1 + radius, y1,
             x1 + radius, y1,
             x2 - radius, y1,
             x2 - radius, y1,
             x2, y1,
             x2, y1 + radius,
-            x2, y1 + radius,
             x2, y2 - radius,
             x2, y2 - radius,
             x2, y2,
             x2 - radius, y2,
-            x2 - radius, y2,
             x1 + radius, y2,
             x1 + radius, y2,
             x1, y2,
@@ -170,6 +303,46 @@ class spacrButton(tk.Frame):
             x1, y1
         ]
         return self.canvas.create_polygon(points, **kwargs, smooth=True)
+    
+    def update_description(self, event):
+        parent = self.master
+        while parent:
+            if hasattr(parent, 'show_description'):
+                parent.show_description(parent.main_buttons.get(self, "No description available."))
+                return
+            parent = parent.master
+
+    def clear_description(self, event):
+        parent = self.master
+        while parent:
+            if hasattr(parent, 'clear_description'):
+                parent.clear_description()
+                return
+            parent = parent.master
+
+    def animate_zoom(self, target_scale, steps=10, delay=10):
+        current_scale = 1.1 if self.is_zoomed_in else 1.0
+        step_scale = (target_scale - current_scale) / steps
+        self._animate_step(current_scale, step_scale, steps, delay)
+
+    def _animate_step(self, current_scale, step_scale, steps, delay):
+        if steps > 0:
+            new_scale = current_scale + step_scale
+            self.zoom_icon(new_scale)
+            self.after(delay, self._animate_step, new_scale, step_scale, steps - 1, delay)
+        else:
+            self.is_zoomed_in = not self.is_zoomed_in
+
+    def zoom_icon(self, scale_factor):
+        # Resize the original icon image
+        new_size = int(self.size * 0.9 * scale_factor)
+        resized_icon = self.original_icon_image.resize((new_size, new_size), Image.Resampling.LANCZOS)
+        self.icon_photo = ImageTk.PhotoImage(resized_icon)
+
+        # Update the icon on the canvas
+        self.canvas.itemconfig(self.button_icon, image=self.icon_photo)
+        self.canvas.image = self.icon_photo  # Keep a reference to avoid garbage collection
+
 
 class spacrSwitch(ttk.Frame):
     def __init__(self, parent, text="", variable=None, command=None, *args, **kwargs):
@@ -177,17 +350,20 @@ class spacrSwitch(ttk.Frame):
         self.text = text
         self.variable = variable if variable else tk.BooleanVar()
         self.command = command
-        self.canvas = tk.Canvas(self, width=40, height=20, highlightthickness=0, bd=0, bg="black")
+        self.canvas = tk.Canvas(self, width=40, height=20, highlightthickness=0, bd=0)
         self.canvas.grid(row=0, column=1, padx=(10, 0))
         self.switch_bg = self.create_rounded_rectangle(2, 2, 38, 18, radius=9, outline="", fill="#fff")
-        self.switch = self.canvas.create_oval(4, 4, 16, 16, outline="", fill="#800080")  # Purple initially
-        self.label = spacrLabel(self, text=self.text, background="black", foreground="white")
+        self.switch = self.canvas.create_oval(4, 4, 16, 16, outline="", fill="#800080")
+        self.label = spacrLabel(self, text=self.text)
         self.label.grid(row=0, column=0, padx=(0, 10))
         self.bind("<Button-1>", self.toggle)
         self.canvas.bind("<Button-1>", self.toggle)
         self.label.bind("<Button-1>", self.toggle)
         self.update_switch()
 
+        style = ttk.Style()
+        _ = set_dark_style(style, containers=[self], widgets=[self.canvas, self.label])
+
     def toggle(self, event=None):
         self.variable.set(not self.variable.get())
         self.animate_switch()
@@ -196,19 +372,19 @@ class spacrSwitch(ttk.Frame):
 
     def update_switch(self):
         if self.variable.get():
-            self.canvas.itemconfig(self.switch, fill="#008080")  # Teal
-            self.canvas.coords(self.switch, 24, 4, 36, 16)  # Move switch to the right
+            self.canvas.itemconfig(self.switch, fill="#008080")
+            self.canvas.coords(self.switch, 24, 4, 36, 16)
         else:
-            self.canvas.itemconfig(self.switch, fill="#800080")  # Purple
-            self.canvas.coords(self.switch, 4, 4, 16, 16)  # Move switch to the left
+            self.canvas.itemconfig(self.switch, fill="#800080")
+            self.canvas.coords(self.switch, 4, 4, 16, 16)
 
     def animate_switch(self):
         if self.variable.get():
             start_x, end_x = 4, 24
-            final_color = "#008080"  # Teal
+            final_color = "#008080"
         else:
             start_x, end_x = 24, 4
-            final_color = "#800080"  # Purple
+            final_color = "#800080"
 
         self.animate_movement(start_x, end_x, final_color)
 
@@ -217,7 +393,7 @@ class spacrSwitch(ttk.Frame):
         for i in range(start_x, end_x, step):
             self.canvas.coords(self.switch, i, 4, i + 12, 16)
             self.canvas.update()
-            self.after(10)  # Small delay for smooth animation
+            self.after(10)
         self.canvas.itemconfig(self.switch, fill=final_color)
 
     def get(self):
@@ -227,7 +403,7 @@ class spacrSwitch(ttk.Frame):
         self.variable.set(value)
         self.update_switch()
 
-    def create_rounded_rectangle(self, x1, y1, x2, y2, radius=9, **kwargs):  # Smaller radius for smaller switch
+    def create_rounded_rectangle(self, x1, y1, x2, y2, radius=9, **kwargs):
         points = [x1 + radius, y1,
                   x1 + radius, y1,
                   x2 - radius, y1,
@@ -265,17 +441,18 @@ class spacrToolTip:
         self.tooltip_window = tk.Toplevel(self.widget)
         self.tooltip_window.wm_overrideredirect(True)
         self.tooltip_window.wm_geometry(f"+{x}+{y}")
-        self.tooltip_window.configure(bg='black')
-        label = tk.Label(self.tooltip_window, text=self.text, background="#333333", foreground="white", relief='flat', borderwidth=0)
+        label = tk.Label(self.tooltip_window, text=self.text, relief='flat', borderwidth=0)
         label.grid(row=0, column=0, padx=5, pady=5)
 
+        style = ttk.Style()
+        _ = set_dark_style(style, containers=[self.tooltip_window], widgets=[label])
+
     def hide_tooltip(self, event):
         if self.tooltip_window:
             self.tooltip_window.destroy()
         self.tooltip_window = None
 
-class modify_masks:
-
+class ModifyMaskApp:
     def __init__(self, root, folder_path, scale_factor):
         self.root = root
         self.folder_path = folder_path
@@ -1119,7 +1296,7 @@ class modify_masks:
                 self.mask[labeled_mask == i] = 0  # Remove small objects
         self.update_display()
 
-class ImageApp:
+class AnnotateApp:
     def __init__(self, root, db_path, src, image_type=None, channels=None, grid_rows=None, grid_cols=None, image_size=(200, 200), annotation_column='annotate', normalize=False, percentiles=(1,99), measurement=None, threshold=None):
         self.root = root
         self.db_path = db_path
@@ -1383,7 +1560,7 @@ class ImageApp:
                 break
 
             if not self.update_queue.empty():
-                ImageApp.update_html("Do not exit, Updating database...")
+                AnnotateApp.update_html("Do not exit, Updating database...")
                 self.status_label.config(text='Do not exit, Updating database...')
 
                 pending_updates = self.update_queue.get()
@@ -1394,7 +1571,7 @@ class ImageApp:
                         c.execute(f'UPDATE png_list SET {self.annotation_column} = ? WHERE png_path = ?', (new_annotation, path))
                 conn.commit()
 
-                ImageApp.update_html('')
+                AnnotateApp.update_html('')
                 self.status_label.config(text='')
                 self.root.update()
             time.sleep(0.1)
@@ -1465,35 +1642,4 @@ def create_menu_bar(root):
     app_menu.add_separator()
     app_menu.add_command(label="Exit", command=root.quit)
     # Configure the menu for the root window
-    root.config(menu=menu_bar)
-
-
-def set_dark_style(style):
-    font_style = tkFont.Font(family="Helvetica", size=24)
-    style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', fieldbackground='black', foreground='#ffffff', font=font_style)
-    style.configure('TCombobox', fieldbackground='black', background='black', foreground='#ffffff', selectbackground='black', selectforeground='#ffffff', font=font_style)
-    style.map('TCombobox', fieldbackground=[('readonly', 'black')], foreground=[('readonly', '#ffffff')], selectbackground=[('readonly', 'black')], selectforeground=[('readonly', '#ffffff')])
-    style.configure('Custom.TButton', background='black', foreground='white', bordercolor='white', focusthickness=3, focuscolor='white', font=('Helvetica', 12))
-    style.map('Custom.TButton', background=[('active', 'teal'), ('!active', 'black')], foreground=[('active', 'white'), ('!active', 'white')], bordercolor=[('active', 'white'), ('!active', 'white')])
-    style.configure('Custom.TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background='black', foreground='#ffffff', font=font_style)
-    style.configure('Spacr.TCheckbutton', background='black', foreground='#ffffff', indicatoron=False, relief='flat', font="15")
-    style.map('Spacr.TCheckbutton', background=[('selected', 'black'), ('active', 'black')], foreground=[('selected', '#ffffff'), ('active', '#ffffff')])
-    style.configure('TLabel', background='black', foreground='#ffffff', font=font_style)
-    style.configure('TFrame', background='black')
-    style.configure('TPanedwindow', background='black')
-    style.configure('TNotebook', background='black', tabmargins=[2, 5, 2, 0])
-    style.configure('TNotebook.Tab', background='black', foreground='#ffffff', padding=[5, 5], font=font_style)
-    style.map('TNotebook.Tab', background=[('selected', '#555555'), ('active', '#555555')], foreground=[('selected', '#ffffff'), ('active', '#ffffff')])
-    style.configure('TButton', background='black', foreground='#ffffff', padding='5 5 5 5', font=font_style)
-    style.map('TButton', background=[('active', '#555555'), ('disabled', '#333333')])
-    style.configure('Vertical.TScrollbar', background='black', troughcolor='black', bordercolor='black')
-    style.configure('Horizontal.TScrollbar', background='black', troughcolor='black', bordercolor='black')
-    style.configure('Custom.TLabelFrame', font=('Helvetica', 10, 'bold'), background='black', foreground='white', relief='solid', borderwidth=1)
-    style.configure('Custom.TLabelFrame.Label', background='black', foreground='white', font=('Helvetica', 10, 'bold'))
-
-def set_default_font(root, font_name="Helvetica", size=12):
-    default_font = (font_name, size)
-    root.option_add("*Font", default_font)
-    root.option_add("*TButton.Font", default_font)
-    root.option_add("*TLabel.Font", default_font)
-    root.option_add("*TEntry.Font", default_font)
+    root.config(menu=menu_bar)

spacr/gui_utils.py

@@ -3,7 +3,7 @@ import tkinter as tk
 from tkinter import ttk
 
 from . gui_core import initiate_root
-from .gui_elements import spacrLabel, spacrCheckbutton, ImageApp
+from .gui_elements import spacrLabel, spacrCheckbutton, AnnotateApp
 
 try:
     ctypes.windll.shcore.SetProcessDpiAwareness(True)
@@ -202,7 +202,7 @@ def annotate(settings):
 
     root = tk.Tk()
     root.geometry(settings['geom'])
-    app = ImageApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], grid_rows=settings['rows'], grid_cols=settings['columns'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'])
+    app = AnnotateApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], grid_rows=settings['rows'], grid_cols=settings['columns'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'])
     next_button = tk.Button(root, text="Next", command=app.next_page)
     next_button.grid(row=app.grid_rows, column=app.grid_cols - 1)
     back_button = tk.Button(root, text="Back", command=app.previous_page)
@@ -302,7 +302,7 @@ def annotate_with_image_refs(settings, root, shutdown_callback):
     conn.commit()
     conn.close()
 
-    app = ImageApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], grid_rows=settings['rows'], grid_cols=settings['columns'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'])
+    app = AnnotateApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], grid_rows=settings['rows'], grid_cols=settings['columns'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'])
 
     # Set the canvas background to black
     root.configure(bg='black')

spacr/icons/abort.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="48px" viewBox="0 -960 960 960" width="48px" fill="#e8eaed"><path d="M349.5-349.5h262v-262h-262v262ZM480.57-132q-72.94 0-135.93-27.52-62.99-27.53-110.39-74.85-47.4-47.33-74.82-110.1Q132-407.25 132-480.2q0-72.03 27.52-135.59 27.53-63.56 74.85-110.71 47.33-47.15 110.1-74.32Q407.25-828 480.2-828q72.03 0 135.59 27.39 63.57 27.39 110.72 74.35 47.14 46.96 74.31 110.39Q828-552.43 828-480.57q0 72.94-27.27 135.93-27.28 62.99-74.35 110.21-47.08 47.21-110.51 74.82Q552.43-132 480.57-132Zm-.14-22q135.07 0 230.32-95.18Q806-344.37 806-480.43q0-135.07-95-230.32Q616.01-806 480.07-806q-135.57 0-230.82 95Q154-616.01 154-480.07q0 135.57 95.18 230.82Q344.37-154 480.43-154ZM480-480Z"/></svg>

spacr/icons/download.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="48px" viewBox="0 -960 960 960" width="48px" fill="#e8eaed"><path d="M306-306h348v-22H306v22Zm173-132 124-123-16-16-97 97v-214h-22v214l-96-97-16 16 123 123Zm1.3 306q-72.21 0-135.43-27.52-63.22-27.53-110.62-74.85-47.4-47.33-74.82-110.26Q132-407.57 132-479.7q0-72.21 27.52-135.93 27.53-63.72 74.85-110.87 47.33-47.15 110.26-74.32Q407.57-828 479.7-828q72.21 0 135.94 27.39 63.72 27.39 110.87 74.35 47.14 46.96 74.31 110.39Q828-552.43 828-480.3q0 72.21-27.27 135.43-27.28 63.22-74.35 110.62-47.08 47.4-110.51 74.82Q552.43-132 480.3-132Zm-.37-22q135.57 0 230.82-95.18Q806-344.37 806-479.93q0-135.57-95.18-230.82Q615.63-806 480.07-806q-135.57 0-230.82 95.18Q154-615.63 154-480.07q0 135.57 95.18 230.82Q344.37-154 479.93-154Zm.07-326Z"/></svg>

spacr/icons/download_for_offline_100dp_E8EAED_FILL0_wght100_GRAD-25_opsz48.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="48px" viewBox="0 -960 960 960" width="48px" fill="#e8eaed"><path d="M306-306h348v-22H306v22Zm173-132 124-123-16-16-97 97v-214h-22v214l-96-97-16 16 123 123Zm1.3 306q-72.21 0-135.43-27.52-63.22-27.53-110.62-74.85-47.4-47.33-74.82-110.26Q132-407.57 132-479.7q0-72.21 27.52-135.93 27.53-63.72 74.85-110.87 47.33-47.15 110.26-74.32Q407.57-828 479.7-828q72.21 0 135.94 27.39 63.72 27.39 110.87 74.35 47.14 46.96 74.31 110.39Q828-552.43 828-480.3q0 72.21-27.27 135.43-27.28 63.22-74.35 110.62-47.08 47.4-110.51 74.82Q552.43-132 480.3-132Zm-.37-22q135.57 0 230.82-95.18Q806-344.37 806-479.93q0-135.57-95.18-230.82Q615.63-806 480.07-806q-135.57 0-230.82 95.18Q154-615.63 154-480.07q0 135.57 95.18 230.82Q344.37-154 479.93-154Zm.07-326Z"/></svg>

spacr/icons/make_masks.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="48px" viewBox="0 -960 960 960" width="48px" fill="#e8eaed"><path d="M747-671q12.55 0 23.78-10.51Q782-692.01 782-704.98q0-13.72-11.22-23.87Q759.55-739 747-739q-13.7 0-23.85 10.24Q713-718.52 713-704.68q0 12.68 10.15 23.18T747-671Zm-166.09 0q13.67 0 24.38-10.51Q616-692.01 616-704.98q0-13.72-10.71-23.87Q594.59-739 580.93-739q-12.81 0-22.87 10.24T548-704.68q0 12.68 9.84 23.18 9.83 10.5 23.07 10.5ZM570-535h188q-5-25-31.74-42.5-26.75-17.5-62.22-17.5-37.48 0-64.26 17.5Q573-560 570-535ZM296.79-116q-85.29 0-143.54-59.21Q95-234.42 95-318v-239h401v238.53q0 83.89-57.58 143.18Q380.84-116 296.79-116Zm-1.04-35q69.13 0 117.19-49T461-317.77V-522H130v204.23Q130-249 178.31-200q48.3 49 117.44 49ZM664-405q-28.58 0-57.79-8T561-434l2-38q20.4 14 45.33 23 24.94 9 55.67 9 68.65 0 117.33-47.33Q830-534.65 830-603.26V-810H497v189h-35v-224h403v241.53q0 82.89-58.62 140.68Q747.75-405 664-405Zm-449.23 19q13.37 0 23.3-9.59Q248-405.17 248-419q0-13.1-9.84-24.05Q228.33-454 215.09-454q-13.66 0-24.38 10.84Q180-432.32 180-419.39q0 14.09 10.7 23.74 10.7 9.65 24.07 9.65Zm164.9 0q13.07 0 23.2-9.59Q413-405.17 413-419q0-13.1-9.86-24.05Q393.28-454 380-454q-14.12 0-24.56 10.84T345-419.39q0 14.09 10.8 23.74 10.79 9.65 23.87 9.65Zm-82.71 140q37.48 0 64.26-17Q388-280 391-306H203q3 26 29.74 43 26.75 17 64.22 17Zm.04-92Zm367-286Z"/></svg>

spacr/icons/map_barcodes.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="48px" viewBox="0 -960 960 960" width="48px" fill="#e8eaed"><path d="M103-221v-479h71v479h-71Zm103 0v-479h69v479h-69Zm103 0v-479h34v479h-34Zm103 0v-479h68v479h-68Zm103 0v-479h103v479H515Zm137 0v-479h34v479h-34Zm103 0v-479h103v479H755Z"/></svg>

spacr/icons/mask.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="48px" viewBox="0 -960 960 960" width="48px" fill="#e8eaed"><path d="M480-309q48.46 0 84.23-29T610-414H349q9 47 45.77 76T480-309ZM301-591h129q0-27-19.08-46-19.09-19-46.5-19Q337-656 319-637.09q-18 18.92-18 46.09Zm229-1h130q0-27-18.87-45.5-18.88-18.5-46-18.5-27.83 0-46.48 18.41Q530-619.17 530-592Zm-50.2 476q-66.8 0-125.64-25.39t-103.5-70Q206-256 181-315.04 156-374.09 156-442v-402h648v402.09q0 67.91-25.2 127.04-25.21 59.12-69.5 103.5Q665-167 605.8-141.5q-59.21 25.5-126 25.5Zm-.3-35q120.5 0 205-84.59Q769-320.17 769-442v-367H191v366.78Q191-320 274.5-235.5t205 84.5Zm.5-329Z"/></svg>

spacr/icons/measure.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="48px" viewBox="0 -960 960 960" width="48px" fill="#e8eaed"><path d="m90-271-28-22 171-275 119.14 140L512-684l85 127q-7.71 3.67-16.79 6.17-9.07 2.5-16.21 6.83l-51-75-152.11 250L239-510 90-271ZM872-63 728-206q-19 14-38.33 20-19.32 6-40.67 6-54.92 0-92.96-38.06-38.04-38.06-38.04-93t38.06-93.44q38.06-38.5 93-38.5t93.44 38.33Q781-366.33 781-311q0 23-7 43t-22 37.45L897-88l-25 25ZM648.86-215q40.08 0 68.61-28.1T746-310.86q0-40.08-28.4-68.61T649.1-408q-40.1 0-68.1 28.4-28 28.4-28 68.5t28.1 68.1q28.1 28 67.76 28ZM720-555q-11-3-20.6-3.45-9.59-.46-17.4-.55l188-299 29 22-179 281Z"/></svg>

spacr/icons/play_circle_100dp_E8EAED_FILL0_wght100_GRAD-25_opsz48.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="48px" viewBox="0 -960 960 960" width="48px" fill="#e8eaed"><path d="m407-351 202-129-202-129v258Zm73.3 219q-72.21 0-135.43-27.52-63.22-27.53-110.62-74.85-47.4-47.33-74.82-110.26Q132-407.57 132-479.7q0-72.21 27.52-135.93 27.53-63.72 74.85-110.87 47.33-47.15 110.26-74.32Q407.57-828 479.7-828q72.21 0 135.94 27.39 63.72 27.39 110.87 74.35 47.14 46.96 74.31 110.39Q828-552.43 828-480.3q0 72.21-27.27 135.43-27.28 63.22-74.35 110.62-47.08 47.4-110.51 74.82Q552.43-132 480.3-132Zm-.37-22q135.57 0 230.82-95.18Q806-344.37 806-479.93q0-135.57-95.18-230.82Q615.63-806 480.07-806q-135.57 0-230.82 95.18Q154-615.63 154-480.07q0 135.57 95.18 230.82Q344.37-154 479.93-154Zm.07-326Z"/></svg>

spacr/icons/run.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="48px" viewBox="0 -960 960 960" width="48px" fill="#e8eaed"><path d="m407-351 202-129-202-129v258Zm73.3 219q-72.21 0-135.43-27.52-63.22-27.53-110.62-74.85-47.4-47.33-74.82-110.26Q132-407.57 132-479.7q0-72.21 27.52-135.93 27.53-63.72 74.85-110.87 47.33-47.15 110.26-74.32Q407.57-828 479.7-828q72.21 0 135.94 27.39 63.72 27.39 110.87 74.35 47.14 46.96 74.31 110.39Q828-552.43 828-480.3q0 72.21-27.27 135.43-27.28 63.22-74.35 110.62-47.08 47.4-110.51 74.82Q552.43-132 480.3-132Zm-.37-22q135.57 0 230.82-95.18Q806-344.37 806-479.93q0-135.57-95.18-230.82Q615.63-806 480.07-806q-135.57 0-230.82 95.18Q154-615.63 154-480.07q0 135.57 95.18 230.82Q344.37-154 479.93-154Zm.07-326Z"/></svg>

spacr/icons/sequencing.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="48px" viewBox="0 -960 960 960" width="48px" fill="#e8eaed"><path d="M246-80v-20q0-141.45 56.5-215.72Q359-390 455-480q-97-90-153.5-164.28Q245-718.55 245-860v-21h34.66v21q0 17 1.08 33.5Q281.83-810 286-796h388.14q2.93-14 4.4-30.5Q680-843 680-860v-21h35v21q0 141.45-57 215.72Q601-570 506-480q95 89 152 163.78 57 74.77 57 216.22v20h-34.66v-20q0-17-1.58-33.5Q677.17-150 674-164H286.86q-3.93 14-4.9 30.5Q281-117 281-100v20h-35Zm99-565h269.18q18.82-25 33.32-54t23.5-62H290q7 34.65 21.25 62.86Q325.5-669.92 345-645Zm135 141q31.34-29.33 58.17-54.67Q565-584 588-610H371q22.75 26.33 50.25 51.67Q448.76-533 480-504ZM372-350h216q-23-26-49.83-51.33Q511.34-426.67 480-457q-31.34 30.33-58.17 55.67Q395-376 372-350Zm-81 151h380q-9-34.5-23.25-62.76Q633.5-290.03 614-315H346q-18.97 24.67-33.48 53.83Q298-232 291-199Z"/></svg>

spacr/icons/settings.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="48px" viewBox="0 -960 960 960" width="48px" fill="#e8eaed"><path d="m421.5-132-15-110.94Q383-249.5 355-265.5t-47.25-34l-101.25 46-59-105 90-66.5q-2.5-13.48-3.75-26.99-1.25-13.51-1.25-27.01 0-12 1.25-26t3.25-30l-89.5-68.5 59-102 101 44q21.5-17 47.5-32.5t50.5-22.5l16-111.5h118l15 112q26 9.5 49.25 23T649-661.5l106.5-44 58 102-94 70.54q3 14.96 4.5 27.96t1.5 24.75q0 10.75-1.75 23.84T719-426.42l93 67.92-59 105-104-47q-22.97 20.36-46.49 35.18Q579-250.5 554.5-244l-15 112h-118Zm17.74-22h80.79l15.69-111.5q29.86-8.07 54.11-21.69Q614.08-300.82 641-326l102.5 44 39.5-68.51L693-418q3.5-19 6-33.71t2.5-28.66q0-16.13-2.25-29.88T693-540l92-69-39.5-69-105 44q-19-20-49.75-39t-56.25-22.5L521.43-806H439l-11.5 110.07q-33 6.43-58.25 20.68T318-635l-102.5-43-40.5 69 90.5 65.5q-5 14-7 30.14t-2 33.83q0 17.03 1.75 31.78T264-418l-89 67 40.14 69 102.36-43q23.5 25.5 49.5 39.25T426.28-264l12.96 110Zm38.25-241q36.05 0 60.53-24.5Q562.5-444 562.5-480T538-540.5Q513.5-565 477.5-565T417-540.5Q392.5-516 392.5-480t24.5 60.5q24.5 24.5 60.49 24.5Zm3.01-85.5Z"/></svg>

spacr/icons/settings_100dp_E8EAED_FILL0_wght100_GRAD-25_opsz48.svg

@@ -0,0 +1 @@
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spacr/icons/stop_circle_100dp_E8EAED_FILL0_wght100_GRAD-25_opsz48.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="48px" viewBox="0 -960 960 960" width="48px" fill="#e8eaed"><path d="M349.5-349.5h262v-262h-262v262ZM480.57-132q-72.94 0-135.93-27.52-62.99-27.53-110.39-74.85-47.4-47.33-74.82-110.1Q132-407.25 132-480.2q0-72.03 27.52-135.59 27.53-63.56 74.85-110.71 47.33-47.15 110.1-74.32Q407.25-828 480.2-828q72.03 0 135.59 27.39 63.57 27.39 110.72 74.35 47.14 46.96 74.31 110.39Q828-552.43 828-480.57q0 72.94-27.27 135.93-27.28 62.99-74.35 110.21-47.08 47.21-110.51 74.82Q552.43-132 480.57-132Zm-.14-22q135.07 0 230.32-95.18Q806-344.37 806-480.43q0-135.07-95-230.32Q616.01-806 480.07-806q-135.57 0-230.82 95Q154-616.01 154-480.07q0 135.57 95.18 230.82Q344.37-154 480.43-154ZM480-480Z"/></svg>

spacr/icons/theater_comedy_100dp_E8EAED_FILL0_wght100_GRAD200_opsz48.svg

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